EarthCube Building Blocks: Collaborative Proposal: GeoTrust: Improving Sharing and Reproducibility of Geoscience Applications

EarthCube 构建模块：协作提案：GeoTrust：提高地球科学应用的共享性和可重复性

• 批准号: 1639759
• 负责人: Tanu Malik
• 金额: $ 78.4万
• 依托单位: DePaul University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-01 至 2021-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1639759&HistoricalAwards=false
• 关键词: EarthCube; Building; Blocks; Collaborative; Proposal

Scientific reproducibility -- the ability to independently verify the work of other scientists -- continues to be a critical barrier towards achieving the vision of cross-disciplinary science. Federal agencies and publishers increasingly mandate and incentivize scientists to, at a minimum, establish computational reproducibility of scientific experiments. To comply scientists must connect descriptions of scientific experiments in scholarly publications with the underlying data and code used to produce the published results and findings. However, in practice, computational reproducibility is hard to achieve since it entails isolating necessary and sufficient computational artifacts and then preserving those artifacts in a standard way for later re-execution. Both isolation and preservation present challenges in large part due to the complexity of existing software and systems as well as the implicit dependencies, resource distribution, and shifting compatibility of systems that evolve over time -- all of which conspire to break the reproducibility of an experiment. The goal of the GeoTrust project is to understand the research lifecycle of scientific experiments from conception to publication and establish a framework that will improve their reproducibility. GeoTrust will develop sandboxing-based systems and tools that help scientists effectively isolate computational artifacts associated with an experiment, use languages and semantics to preserve artifacts, and re-execute /reproduce experiments by deploying the artifacts, changing datasets, algorithms, models, environments, etc. This reproducible framework will be adopted by and integrated within community infrastructures of three geoscience sub-disciplines viz. Hydrology, Solid Earth, and Space Science. Using cross-disciplinary science uses cases from these sub-disciplines, and engaging independent evaluators, we will assess the effectiveness of the framework in achieving reproducibility of computational experiments. Finally, verified results will be associated with ?stamps of reproducibility?, establishing community recognition of computational experiments. The framework will be developed as an EarthCube capability, with software developed and released as per EarthCube requirements. Early adopters across other geoscience sub-disciplines will be continually sought.

科学可重复性——独立验证其他科学家工作的能力——仍然是实现跨学科科学愿景的关键障碍。联邦机构和出版商越来越多地要求和激励科学家至少建立科学实验的计算可重复性。为了遵守规定，科学家必须将学术出版物中科学实验的描述与用于产生已发表结果和发现的基础数据和代码联系起来。然而，在实践中，计算可再现性很难实现，因为它需要隔离必要且足够的计算工件，然后以标准方式保留这些工件以供以后重新执行。隔离和保存都面临挑战，很大程度上是由于现有软件和系统的复杂性，以及隐含的依赖性、资源分布和随时间演变的系统兼容性——所有这些都共同破坏了实验的可重复性。 GeoTrust 项目的目标是了解科学实验从构思到发表的研究生命周期，并建立一个提高其可重复性的框架。 GeoTrust 将开发基于沙箱的系统和工具，帮助科学家有效隔离与实验相关的计算工件，使用语言和语义来保留工件，并通过部署工件、更改数据集、算法、模型、环境来重新执行/重现实验，这个可重复的框架将被三个地球科学子学科（即地球科学子学科）的社区基础设施采用并集成到其中。水文学、固体地球和空间科学。利用来自这些子学科的跨学科科学用例，并聘请独立评估者，我们将评估该框架在实现计算实验的可重复性方面的有效性。最后，经过验证的结果将与“再现性标记”相关联，从而建立计算实验的社区认可。该框架将作为 EarthCube 功能进行开发，并根据 EarthCube 要求开发和发布软件。我们将不断寻找其他地球科学子学科的早期采用者。

项目成果

Integrating scientific cyberinfrastructures to improve reproducibility in computational hydrology: Example for HydroShare and GeoTrust

集成科学网络基础设施以提高计算水文学的可重复性：HydroShare 和 GeoTrust 示例

• DOI: 10.1016/j.envsoft.2018.03.025
• 发表时间: 2018-07
• 期刊: Environmental Modelling & Software
• 影响因子: 4.9
• 作者: Essawy, Bakinam T.;Goodall, Jonathan L.;Zell, Wesley;Voce, Daniel;Morsy, Mohamed M.;Sadler, Jeffrey;Yuan, Zhihao;Malik, Tanu
• 通讯作者: Malik, Tanu

Efficient Provenance Alignment in Reproduced Executions

复制执行中的高效出处对齐

• 发表时间: 2020-01
• 期刊: USENIX Theory and Practice of Provenance
• 作者: Y. Nakamura; T. Malik
• 通讯作者: T. Malik

SciInc: A Container Runtime for Incremental Recomputation

SciInc：用于增量重新计算的容器运行时

• DOI: 10.1109/escience.2019.00040
• 发表时间: 2019-01
• 期刊: IEEE 15th International Conference on eScience
• 作者: A. Youngdahl; D.H. Ton
• 通讯作者: D.H. Ton

Utilizing Provenance in Reusable Research Objects

利用可重复使用的研究对象的来源

• DOI: 10.3390/informatics5010014
• 发表时间: 2018-03
• 期刊: Informatics
• 作者: Yuan, Zhihao;Ton That, Dai;Kothari, Siddhant;Fils, Gabriel;Malik, Tanu
• 通讯作者: Malik, Tanu

Sciunits: Reusable Research Objects

Sciunits：可重复使用的研究对象

• DOI: 10.1109/escience.2017.51
• 发表时间: 2017-10
• 期刊: IEEE 13th International Conference on e-Science (e-Science
• 作者: Ton That, Dai Hai;Fils, Gabriel;Yuan, Zhihao;Malik, Tanu
• 通讯作者: Malik, Tanu